[gmx-users] problem in md of methanol box

[David van der Spoel]

On Fri, 2002-09-27 at 11:02, 刘 松柏 wrote:
> hi, everyone. I met a problem when I tried to run equilibrated md of 
> methanol box which was generated from spc216.gro by replacing one hydrogen 
> by CH3, adjusting density to 790 and subsequent em. The .mdp file for md is 
> the water.mdp released by gromacs. The following warning jumped out as md 
> was running.  I don't what's wrong.
That means large forces, and hence that minimization was not good
enough. Are you shure you used the output from em as input to md? If so,
you could try a short run without pressure coupling.

Please do also check which forcefield you are using. There has been some
discussion on the list a couple of months ago.

> 
> Thanks for any opinion!
> 
> 
> Warning: Only triclinic boxes with the first vector parallel to the x-axis 
> and the second vector in the xy-plane are supported.
>          Box (3x3):
>             Box[    0]={         nan,          nan,          nan}
>             Box[    1]={         nan,          nan,          nan}
>             Box[    2]={         nan,          nan,          nan}
>          Can not fix pbc.
> Warning: Only triclinic boxes with the first vector parallel to the x-axis 
> and the second vector in the xy-plane are supported.
>          Box (3x3):
>             Box[    0]={         nan,          nan,          nan}
>             Box[    1]={         nan,          nan,          nan}
>             Box[    2]={         nan,          nan,          nan}
>          Can not fix pbc.
> Warning: Only triclinic boxes with the first vector parallel to the x-axis 
> and the second vector in the xy-plane are supported.
>          Box (3x3):
>             Box[    0]={         nan,          nan,          nan}
>             Box[    1]={         nan,          nan,          nan}
>             Box[    2]={         nan,          nan,          nan}
>          Can not fix pbc.
> 
> 
> 
> 
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel
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